Use jupyter notebook for CT reconstruction

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Jiao edited this page Oct 28, 2016 · 14 revisions

This tutorial is obsolete. Please refer to the new tutorial

Connect to CG1D-analysis2 cluster using thinlinc client or browser (https://cg1d-analysis2.ornl.gov).

All the following actions happen inside the connected thinlinc or browser window.

First start the jupyter notebook if you have not done so
Then make a copy of the notebook template in the notebooks subdir in your home directory in a terminal:

$ cp /HFIR/CG1DImaging/shared/notebook-examples/Cu_block.ipynb \
    ~/notebooks/MySample.ipynb

Open the new notebook by

$ /HFIR/CG1DImaging/shared/open-jupyter-notebook ~/notebooks/MySample.ipynb

A new browser window should show up.

In the browser window for your new notebook, click menu "Kernel" -> "Change kernel" -> "imars3d"
Follow the instructions in the notebook.